Posted on November 30, 2007Description of a unique newly-described virus that looks like a chimaera of a papillomavirus and a polyomavirus

Now that the dust has begun to settle after the launch of Merck’s much-hyped Gardasil genital papillomavirus vaccine – discussed in MicrobiologyBytes here and here – people are turning again to looking at the natural history […]

I inadvertently became a published literary critic a little while ago. A long-time English Department colleague asked me for some help interpreting the collected works of possibly the most important modern poet from South Africa, and […]

Posted on September 14, 2007Description of natural insertions of virus gene fragments into a variety of organisms and how they elicit pathogen-derived resistance

And they’re protecting you! If you’re an insect, that is. Or possibly a plant.
In a remarkable convergence of news, an Israeli group led by Ilan Sela described how Israeli acute paralysis virus, which is implicated in […]

This is the End. Or the beginning of the end. Or possibly, the end of the beginning?
To misquote the immortal Bill Shankly: “It’s not a matter of life and death: it’s much more important than that”.
Having […]

Posted on August 3, 2007News on inferring “ancestor sequences” for HIV to help make broadly effective vaccines

While fossilized viruses have never been found, we can often infer probable lines of evolutionary descent by analysis of extant genomic sequences. This sort of molecular phylogenetic approach has thrown up all sorts of interesting […]

I have been engaging in an interchange of letters in the Weekend Argus here in Cape Town over the last couple of weeks, the subject of which some folk may find enlightening. It seems that, with the governmental decree that all schools in South Africa are now to teach evolution – previously a VERY contentious issue, and often simply not taught – there are a number of folk out there who simply refuse to believe in most or even any evidence for evolution, and who say so to newspapers. Herewith my contributions….

As a practicing biological scientist, I must admit to being alarmed over the tenor of arguments advanced by many believers in fundamental religious teachings, who seem to take it as a given that belief in the teachings contained in especially the Christian Bible are incompatible with “evolutionary theory”. This is very true here in South Africa right now, with news that the Department of Education is going to mandate teaching of evolution to senior secondary school learners.

The central tenet is, of course, simple nonsense – unless you believe that everything in the Bible is literally true. And if you believe that, then – as others have previously pointed out in the context of the Biblical proscription of homosexuality – then you should also believe that slavery is acceptable, that you may kill your neighbour for working on the Sabbath, that you should avoid contact with menstruating women, and that you should not wear glasses when approaching the altar of the Lord, among many other strictures incompatible with modern life. Oh, and that it is perfectly fine to stone your neighbour for wearing clothes made of more than one type of thread. Which doesn’t seem that bad an idea if they are wearing those godawful two-tone shirts from Mr Price…but no, no, perish the thought.

Why do people who presumably accept the fact of gravity not accept the fact of evolution? For all the nonsense written and spoken about evolution, like gravity, it IS a fact. We may argue about exactly how both of them work, which is where theory comes in, but the facts of the phenomena cannot be doubted by anyone who understands the evidence. Which, in the case of gravity, means falling on the floor if you lift both legs up. Unfortunately, evolution is a little harder to demonstrate in action – and denial of its existence has fewer immediate consequences.

But consider this: evidence of micro-evolution happening right now is all around you, in the form of flu and HIV and TB, which persist because the agents continually change so as to avoid their hosts’ immune systems or the drugs designed to combat them. Ignoring the fact of evolution in the case of these three and other disease agents is tantamount to signing a suicide letter on behalf of our species. There is in fact, directly contradictory to many assertions, increasing evidence of past macro-evolution in fossil “transitional forms” of especially vertebrates, which for instance illustrate very clearly just how fish became amphibians. There is a very nice Web page associated with the Public Broadcasting Service (PBS) in the USA, which graphically demonstrates this and other evolutionary facts. Discover magazine also has a very good short article debunking much of what Michael Behe, a renegade biochemist and ardent intelligent designer, has to say in a new book on the limits of Darwinism.

As for new genetic evidence, just today I read in a recent New Scientist (Oct 27) of genetic evidence from modern lungfish pinpointing just how limbs developed from fins, in extinct lobe-finned fish. All in all, we have evidence of well-established life on this planet from over 3 billion years ago – and a pretty clear idea of how we got here from there. Among people who understand the evidence, then, there is no doubt of evolution as a fact. And the nice thing about evolution is that we can always find more evidence for it, palaeontologically and biologically – so that any “theory” (like intelligent design) which exists only in the cracks of the imposing edifice that is evolutionary fact, will inevitably be squeezed to death.

Which is the evolutionary fate of all unfit theories….B-)

In response to subsequent letters, Weekend Argus December 9th 2007:

While I agree with at least some of Bob Holcombe’s letter (Weekend Argus, November 25th)- and in particular, the statement that “…it is good religion in my mind to recognise that evolution is a fact” – I must categorically deny the truth of the serious hurdles he lists in the way of accepting “the macro-evolution theory” (which one??) as fact.As for Dr Bernhard Ficker’s letter, I can only assume that he is stuck in a kind of evolutionary denialism that originated in the 19th century or even earlier, with statements like “only kind begats kind”, which has been thoroughly and comprehensively discredited.

I reiterate here that evolution is a fact, not a theory: the overwhelming majority of scientific professionals who work in especially the biological but also the geological sciences accept this as being irrefutably true, whether one is discussing microevolution (changes that happen in our lifetimes) or macroevolution (changes that happen in geological time).As I mentioned previously (Weekend Argus, Nov 18th), the former is easy to demonstrate, with organisms like viruses and bacteria – which examples do most certainly not lead to degeneration, incidentally.The latter, while harder to show – palaeontology is still an under-funded scientific endeavour – is also amply evidenced: for example, there is an excellent web site which explains in very simple terms a lot of the recent evidence for evolution, and in particular for fossil transitional forms (see here).

The only wiggle-room in our understanding of evolution, then, lies in discussion of the exact mechanisms by which it occurs, and whether or not any particular species or lineage is in fact ancestral to, coincident with, or descended from another.This discussion gives rise to several – not just one – theories of evolution, just as there are a number of theories purporting to explain just how gravity works.Any discussion which refers to “the” theory of evolution, then, is simply uninformed and should be ignored.

Where many lay people are misled in the evolution debates is by accepting monographs as being authoritative evidence of one or other point of view: books can be written by anyone, and most are not refereed before publication – unlike the mainstream scientific literature.Unfortunately, the former is usually much more accessible than the latter, so that most amateurs do not access the kinds of information that scientific professionals do – via the pages of journals such as Nature, Science or even New Scientist or Discover magazines.This leads to the kinds of misinformation that Bob Holcombe refers to, such as the statements thatspontaneous generation (the origin of life) occurred only once, or that there is a problem with the concept that viruses, bacteria, plants and animals are interrelated or that vertebrates evolved from invertebrates.

In fact, some biologists are actively looking for evidence that life may have arisen more than once; there is ample genetic evidence that nearly every type of organism on this planet is related to every other, and many of us are excited at the prospect of finding life off this planet as well.In my own field – virology – there is is excellent genetic evidence pointing to the evolution of my pet organisms over hundreds of millions of years, from progenitors that look very different to what we find today and which may even have originated in cellular lifeforms. It is also now universally accepted among serious biologists that plants originate from two separate unions of different bacteria and an ancestral eukaryote, giving rise to bacterial-descended chloroplasts and mitochondria within another kind of cell, and that we as an organism differ from plants more by not having chloroplasts than by any other intrinsic property.The fact is that ALL cellular organisms share a basic set of 500 genes, or part of the genetic blueprint, which can be shown to be related throughout the tree of life (see here), meaning we are all related to one another here on Mother Earth.

Bob Holcombe mentions Sir Isaac Newton, and how he had “no problem reconciling the physical world with God’s word”.In fact, he went a lot further than that: as an intensely religious man, he embarked on a life-long quest to do exactly this – yet at the same time, was a closet alchemist, which has a belief system at odds with both his religion and his orthodox science.Perhaps we all need to learn to do as he did, then: be prepared to believe in a number of apparently contradictory things simultaneously, so that our religious beliefs need not conflict with scientific evidence.

Biotechnologist and researcher

I have been at UCT since I came to Cape Town on holiday from Zambia in 1974, and fell in love with the place. I obtained a BSc in Chemistry and Microbiology in 1976, an Hons in Virology in 1977, an MSc in Virology in 1979, and a PhD in the same discipline in 1984. I became a Lecturer in Virology in 1981, and have risen through the ranks to become a Professor in Microbiology (in January 2003). I am also a Founder Member of the Institute of Infectious Disease and Molecular Medicine (IIDMM) based in the Health Sciences Faculty.